Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018433.1 Corchorus olitorius cultivar O-4 contig18466, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 21097
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:10295 original size:48 final size:48

Alignment explanation


    Indices: 10242--10333  Score: 157
    Period size: 48  Copynumber: 1.9  Consensus size: 48

      10232 ATAATACCAA

                             *                              
      10242 GGGTGTAAATTCTATTAGAATCATCCTAAAAAGGGGTGTTTTTAGGAT
          1 GGGTGTAAATTCTATTAAAATCATCCTAAAAAGGGGTGTTTTTAGGAT

                                            **          
      10290 GGGTGTAAATTCTATTAAAATCATCCTAAAAATTGGTGTTTTTA
          1 GGGTGTAAATTCTATTAAAATCATCCTAAAAAGGGGTGTTTTTA

      10334 AGATTACATT


Statistics
Matches: 41,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  48   41  1.00

ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38


Consensus pattern (48 bp):   
GGGTGTAAATTCTATTAAAATCATCCTAAAAAGGGGTGTTTTTAGGAT

Found at i:11208 original size:14 final size:14

Alignment explanation


    Indices: 11189--11219  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      11179 CAAAAAGAAC

                          
      11189 ATTTAATTTTAATG
          1 ATTTAATTTTAATG

                          
      11203 ATTTAATTTTAATG
          1 ATTTAATTTTAATG

               
      11217 ATT
          1 ATT

      11220 AGTTTCACCT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58


Consensus pattern (14 bp):   
ATTTAATTTTAATG

Found at i:18091 original size:90 final size:90

Alignment explanation


    Indices: 17938--18118  Score: 335
    Period size: 90  Copynumber: 2.0  Consensus size: 90

      17928 ACTTATAAAT

                                            **                               
      17938 TTTGAATTTAATCTCTTAATGAAGCGACATATTGTGATGGACTGACGGTGTATAGAAACAATACA
          1 TTTGAATTTAATCTCTTAATGAAGCGACATATCATGATGGACTGACGGTGTATAGAAACAATACA

                                     
      18003 CGTCGGTGCATCAAATATTAACCTA
         66 CGTCGGTGCATCAAATATTAACCTA

                                                         *                   
      18028 TTTGAATTTAATCTCTTAATGAAGCGACATATCATGATGGACTGATGGTGTATAGAAACAATACA
          1 TTTGAATTTAATCTCTTAATGAAGCGACATATCATGATGGACTGACGGTGTATAGAAACAATACA

                                     
      18093 CGTCGGTGCATCAAATATTAACCTA
         66 CGTCGGTGCATCAAATATTAACCTA

             
      18118 T
          1 T

      18119 AAATTAAAAA


Statistics
Matches: 88,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  90   88  1.00

ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31


Consensus pattern (90 bp):   
TTTGAATTTAATCTCTTAATGAAGCGACATATCATGATGGACTGACGGTGTATAGAAACAATACA
CGTCGGTGCATCAAATATTAACCTA
Done.